What do you mean by "simulates biology on a molecular level"? There are definitely 3D molecule viewers, as well as programs for organic chemistry mechanisms, but not something that encompasses every detail of all living processes ever.
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LanceLafontaineAug 10 '12 at 1:36

The authors combined 28 different sub-modules of various biological processes from the literature. Each one operates at the level of macromolecules, although models them in different ways: some by ODEs, some by logic; some by agent-based approaches. If you want to fool around their code is available online and I wrote a basic introduction/summary of the paper.

Just a very important note, seen what the OP is asking. Simulating one cell is great, but it does not in any way mean that we can currently simulate an entire organism with that same level of detail.
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nicoOct 16 '12 at 17:41